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JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison

BACKGROUND: Cross-species comparisons of gene neighborhoods (also called genomic contexts) in microbes may provide insight into determining functionally related or co-regulated sets of genes, suggest annotations of previously un-annotated genes, and help to identify horizontal gene transfer events a...

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Detalles Bibliográficos
Autores principales: Seitzer, Phillip, Huynh, Tu Anh, Facciotti, Marc T
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3560190/
https://www.ncbi.nlm.nih.gov/pubmed/23324080
http://dx.doi.org/10.1186/1471-2105-14-18
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author Seitzer, Phillip
Huynh, Tu Anh
Facciotti, Marc T
author_facet Seitzer, Phillip
Huynh, Tu Anh
Facciotti, Marc T
author_sort Seitzer, Phillip
collection PubMed
description BACKGROUND: Cross-species comparisons of gene neighborhoods (also called genomic contexts) in microbes may provide insight into determining functionally related or co-regulated sets of genes, suggest annotations of previously un-annotated genes, and help to identify horizontal gene transfer events across microbial species. Existing tools to investigate genomic contexts, however, lack features for dynamically comparing and exploring genomic regions from multiple species. As DNA sequencing technologies improve and the number of whole sequenced microbial genomes increases, a user-friendly genome context comparison platform designed for use by a broad range of users promises to satisfy a growing need in the biological community. RESULTS: Here we present JContextExplorer: a tool that organizes genomic contexts into branching diagrams. We implement several alternative context-comparison and tree rendering algorithms, and allow for easy transitioning between different clustering algorithms. To facilitate genomic context analysis, our tool implements GUI features, such as text search filtering, point-and-click interrogation of individual contexts, and genomic visualization via a multi-genome browser. We demonstrate a use case of our tool by attempting to resolve annotation ambiguities between two highly homologous yet functionally distinct genes in a set of 22 alpha and gamma proteobacteria. CONCLUSIONS: JContextExplorer should enable a broad range of users to analyze and explore genomic contexts. The program has been tested on Windows, Mac, and Linux operating systems, and is implemented both as an executable JAR file and java WebStart. Program executables, source code, and documentation is available at http://www.bme.ucdavis.edu/facciotti/resources_data/software/.
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spelling pubmed-35601902013-02-04 JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison Seitzer, Phillip Huynh, Tu Anh Facciotti, Marc T BMC Bioinformatics Software BACKGROUND: Cross-species comparisons of gene neighborhoods (also called genomic contexts) in microbes may provide insight into determining functionally related or co-regulated sets of genes, suggest annotations of previously un-annotated genes, and help to identify horizontal gene transfer events across microbial species. Existing tools to investigate genomic contexts, however, lack features for dynamically comparing and exploring genomic regions from multiple species. As DNA sequencing technologies improve and the number of whole sequenced microbial genomes increases, a user-friendly genome context comparison platform designed for use by a broad range of users promises to satisfy a growing need in the biological community. RESULTS: Here we present JContextExplorer: a tool that organizes genomic contexts into branching diagrams. We implement several alternative context-comparison and tree rendering algorithms, and allow for easy transitioning between different clustering algorithms. To facilitate genomic context analysis, our tool implements GUI features, such as text search filtering, point-and-click interrogation of individual contexts, and genomic visualization via a multi-genome browser. We demonstrate a use case of our tool by attempting to resolve annotation ambiguities between two highly homologous yet functionally distinct genes in a set of 22 alpha and gamma proteobacteria. CONCLUSIONS: JContextExplorer should enable a broad range of users to analyze and explore genomic contexts. The program has been tested on Windows, Mac, and Linux operating systems, and is implemented both as an executable JAR file and java WebStart. Program executables, source code, and documentation is available at http://www.bme.ucdavis.edu/facciotti/resources_data/software/. BioMed Central 2013-01-16 /pmc/articles/PMC3560190/ /pubmed/23324080 http://dx.doi.org/10.1186/1471-2105-14-18 Text en Copyright ©2013 Seitzer et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software
Seitzer, Phillip
Huynh, Tu Anh
Facciotti, Marc T
JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison
title JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison
title_full JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison
title_fullStr JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison
title_full_unstemmed JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison
title_short JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison
title_sort jcontextexplorer: a tree-based approach to facilitate cross-species genomic context comparison
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3560190/
https://www.ncbi.nlm.nih.gov/pubmed/23324080
http://dx.doi.org/10.1186/1471-2105-14-18
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